The world of Shining Force EXA has long been steeped in devastating wars and oppression. Two bitter nations wage constant war upon each other by summoning armies of beasts and demons. Now, decades later, neither side has gained any perceivable advantage over the other, while the world and its people lay ravaged and devastated by the ceaseless fighting. Players take the role of two characters in Shining Force EXA; Toma, a warrior who holds the power to wield the Shining Force, is destined to unite the divided world in which he lives; and Cyrille, a powerful sorceress who fights to create a better future for her homeland. Together Toma and Cyrille embark on a quest to bring peace and order back to their war-ravaged world.

Shining Force EXA debuts an innovative Fortress System by which players manage the growth, layout, and defense of the Geo Fortress, the player's home base. As players leave the Geo Fortress to go on missions and quests, they are kept abreast of events at the fortress. If at anytime the Geo Fortress is attacked during the quest, players must switch between parties and use members from the defensive force that were left to protect the fortress from invasion. The Geo Fortress can evolve during the game to match players' personal style and tactics.